User talk:Mark Rust

Formating and markup

Hello Mark Rust, my name is Zach, and I'm on the Exec Board and I'm on the bug tracking team. When you were talking about formatting issues, I haven't looked at the exact pages you're talking about, but there are 2 major issues that probably cover what you're talking about:

1) We're using WP article versions from late September or so. This means that any changes you did on Wikipedia in October or November isn't going to show up here. We're eventually planning to re-import untouched articles from Wikipedia to catch up some of those changes, but that hasn't happened yet. Alternatively, if you want to copy and paste the latest version from Wikipedia, feel free to (our pages already note automatically that the pages are at least partially derived from WP, so that's 100% legitimate if you want to do that).

2) We're not on exactly the same software platform as Wikipedia. We both use the MediaWiki software, but Wikipedia uses a hodgepodge of code modifications and extensions that we need to track down. If there's an up-to-date list of what modifications and extensions WP uses, I haven't seen it. Additionally, we use a different Database from Wikipedia (PostGRE SQL instead of MySQL (which shouldn't affect formatting)). Our tech team is three volunteers (who all have day jobs), so unfortunately, progress is not instantaneous.

As to what you can do, I would recommend worrying about the content over the formatting for the time being (if possible). If you do decide to do some formatting work and can figure out what works and what doesn't, by all means let me know.

Let me know if I can be of further help,

Zach Pruckowski

With regards to your two comments on my talk page:

1) The behavior with <sub> is actually the correct behavior. _{is actually an HTML tag, and you have to "close" it with the} tag or else it just keeps going to the end of the page or paragraph. MediaWiki (the software we use) supports both its own specialized markup (wikitext) which traditionally has identical opening and closing tags (like [[ and ]] (links to other CZ pages) or '' and '' (italic)) and HTML/XHTML/CSS, which have slightly different opening and closing tags (generally <something> to open and </something> to close).

2) You are correct that PNG graphics are not working. There's some sort of program that needs to be installed on our end for PNG support to work. Unfortunately, our technical team (of which I'm not a member fully) is all volunteer, and rather overwhelmed (as they all have full-time jobs, as well as families), so we haven't gotten that change made yet, but we fully intend to eventually (and hopefully soon) support PNG. In the meantime, there exist a lot of free applications for every OS (Windows, Mac, and Linux) that will convert images from PNG to JPEG on your computer, so that'll have to suffice in the short term.

--ZachPruckowski 14:48, 23 December 2006 (CST)

fair use (or unfair use)

There's not much of a consensus as to what to do about fair use images. There's been talk about it on the forums a bit, but we don't have a totally coherent policy. We definitely prefer freely licensed stuff. I'd pose the question on the forum or on the discussion list, and provide as much information as possible about the image. Happy Holidays. --ZachPruckowski 16:52, 23 December 2006 (CST)

Nuclear chemistry

Hi Mark, I noted that you were doing some great stuff, not my field by a long way but I have catholic interests. I can see that as you're writing you're hitting this universal problem of how much detail to include. The problem is as you fill one section with detail you'll need to fill the others similarly or the article will feel unbalanced. I think a good way, as you've indicated, is to write the first article as an introductory overview, not assuming too much technical knowledge but giving glimpses of sophistication, and then to feed into maybe short more technical articles. Again, I think the key is to ask who is going to read this and why? Whatever your answer the answer is fine, but have that clear in your mind and flag it on the Talk page. Happy christmas!Gareth Leng 14:20, 25 December 2006 (CST)

---

Greetings Mark! I've been surfing "articles to approve" and came upon Nuclear Chemistry. I see that its still going through some growing. Just a quick reminder about how the approval process is working. You can't actually nominate an article for approval if you've done all the work on it - or rather, you need to nominate it with other editors from your work group (or in this case physics, chemistry.. related workgroups). You need to rustle up some other editors to read through and give it the stamp (it's helpful if they say something in the discussion page) before we approve the article. Thanks for the hard work. It looks great. -- Sarah Tuttle 12:43, 29 December 2006 (CST)

Mark, I was pleased by your invitation. I noticed your recurrent "nuclear chemistry" on "recent changes", but have been making some scattershot changes of my own and hadn't got around to look at the article yet. I will do so within the next couple of days, and I will spend some time when I do - simultaneously doing some library research to add medical stuff. I'll also ask other health science editors. Thanks, Nancy Sculerati MD 07:48, 30 December 2006 (CST)

Hello! How many active chemistry editors do we have now? Keep up the great work! -Tom Kelly (Talk) 18:15, 14 January 2007 (CST)

Radiolysis and deeep subsurface energy sources for life

The yield and isotopic composition of radiolytic H2, a potential energy source for the deep subsurface biosphere LI-HUNG LIN,1,*† GREG F. SLATER,2,3 BARBARA SHERWOOD LOLLAR,2 GEORGES LACRAMPE-COULOUME,2 and T. C. ONSTOTT1 Geochimica et Cosmochimica Acta, Vol. 69, No. 4, pp. 893–903, 2005

http://deepbio.princeton.edu/samp/papers/LinetalGCA69-893.pdf

Note implied deep bio web page at Princetomn 1Department of Geosciences, Princeton University, Princeton, NJ, USA 2Stable Isotope Laboratory, Department of Geology, University of Toronto, Toronto, ON, Canada 3Woods Hole Oceanographic Institute, Woods Hole, MA, USA (Received February 12, 2004; accepted in revised form July 29, 2004)

... H2 production through abiotic processes is critical to maintaining an H2-based subsurface lithoautotrophic ecosystem that is independent from surface photosynthesis. H2 constitutes a major component of dissolved inorganic gases (as high as 98% by volume of the total dissolved gases) in the groundwater of Precambrian Shields, and its concentration ranges up to several mM (Haveman and Pedersen, 1999; Sherwood Lollar et al., 1993a; Sherwood Lollar et al., 1993b).

... observed in the studies for marine sediments or shallow aquifers (Hoehler et al., 1998; Lovely and Goodwin, 1988). Radiolysis of water has been proposed as a mechanism for generating these large quantities of H2 (Savary and Pagel, 1997; Vovk, 1982). This hypothesis is supported by the observation that H2-bearing fluid inclusions in quartz are associated with U-bearing minerals (Debussy et al., 1988; Savary and Pagel, 1997). Cites: Savary V. and Pagel M. (1997) The effects of water radiolysis on local redox conditions in the Oklo, Gabon, natural fission reactors 10 and 16. Geochim. Cosmochim. Acta 61, 4479–4494. Vovk I. F. (1982) Radiolysis of underground waters as the mechanism of geochemical transformation of the energy of radioactive decay in sedimentary rocks. Litho. Mineral. Res. 16, 328–334.

Energy released from the decay of radioactive elements (e.g., U, Th, and K) dissociates water molecules into H●, OH●, H2, H2O2, a hydrous electron (eaq �), and H� (reaction 1 in Table 1). These products are formed within �10�6 s after the primary ionizing event and diffuse into the bulk solution where they react with other aqueous species (see reactions in Table 1). Additional H2 is formed via the subsequent recombination of ...

Geomicrobiology Journal Issue: Volume 23, Number 6 / September 2006 Pages: 345 - 356 URL: Linking OptionsDOI: 10.1080/01490450600875571 Geomicrobial Processes and Biodiversity in the Deep Terrestrial Subsurface

The Deep Hot Biosphere T Gold, FFRW Dyson - 1998 - ... sulfur or sul- fides such as hydrogen sulfide and ... the earth and that a primordial source of hydrocarbons ... expansion of terrestrial life, then subsurface life on ...

Is H2 the Universal Energy Source for Long-Term Survival? Journal Microbial Ecology Issue Volume 38, Number 4 / November, 1999 DOI 10.1007/s002489901002 Pages 307-320 SpringerLink Date Thursday, February 19, 2004 James K. Fredrickson A1 and David L. Balkwill A2 Keywords: lithoautotrophy, hydrogen, phylogeny, community structure, repository

A hydrogen-based subsurface microbial community dominated by methanogens Francis H. Chapelle*, Kathleen O'Neill², Paul M. Bradley*, Barbara A. Methe², Stacy A. Ciufo², LeRoy L. Knobel³ & Derek R. Lovley²

• US Geological Survey, Columbia, South Carolina 29210, USA

² Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, USA ³ US Geological Survey, Idaho Falls, Idaho 83402, USA http://wetlands.ifas.ufl.edu/sickman/SOS%206932/Ocean%20vent%20papers.pdf

McCollom, T. M. Methanogenesis as a potential source of chemical energy for primary biomass production by autotrophic organisms in hydrothermal systems on Europa. J. Geophys. Res. 104 (E12), 30729±30742 (1999).

McKay, C. P. in Subsurface Microbiology and Biogeochemistry (eds Fredrickson, J. K. & Fletcher, M.) 315±327 (Wiley, New York, 2001).

http://aem.asm.org/cgi/content/abstract/68/12/6013 Applied and Environmental Microbiology, December 2002, p. 6013-6020, Vol. 68, No. 12 0099-2240/02/$04.00+0 DOI: 10.1128/AEM.68.12.6013-6020.2002 Isolation and Characterization of Metal-Reducing Thermoanaerobacter Strains from Deep Subsurface Environments of the Piceance Basin, Colorado Yul Roh, Shi V. Liu,{dagger} Guangshan Li, Heshu Huang, Tommy J. Phelps, and Jizhong Zhou*

Philos Trans R Soc Lond B Biol Sci. 2006 Oct 29;361(1474):1819-34; discussion 1835-6. Early anaerobic metabolisms. Canfield DE, Rosing MT, Bjerrum C. Nordic Centre for Earth Evolution (NordCEE) and Institute of Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark. [email protected]

Before the advent of oxygenic photosynthesis, the biosphere was driven by anaerobic metabolisms. We catalogue and quantify the source strengths of the most probable electron donors and electron acceptors that would have been available to fuel early-Earth ecosystems. The most active ecosystems were probably driven by the cycling of H2 and Fe2+ through primary production...

PMID 17008221

Met Ions Biol Syst. 2005;43:9-48. Biogeochemistry of dihydrogen (H2). Hoehler TM.

Hydrogen has had an important and evolving role in Earth's geo- and biogeochemistry, from prebiotic to modern times. On the earliest Earth, abiotic sources of H2 were likely stronger than in the present...

As one of the dominant sources of biological productivity for as much as 2 billion years of Earth's history, these communities have been among the most important agents of long-term global biogeochemical change.

PMID 16370113 David Tribe 22:18, 18 January 2007 (CST)